Download the source code here: samtools-1.22.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)

Bug fixes:

• SECURITY: Fix use-after-free bug in samtools mpileup -a due to reference sequences being discarded too early. This could happen when the -a option was used, and all the alignments for one of the references started at the same position. This caused mpileup to try to load the next reference before it had finished writing data for the previous one out. (PR #2229, fixes #2227. Reported by Pouya Kheradpour)

• This release bundles htslib-1.22.1 and htscodecs v1.6.4. Fixes a possible buffer overflow on some invalid CRAM inputs; and a failure when trying to save data with very long alignment records with sequence '*' as CRAM version 3.1.
  See the HTSlib and htscodecs NEWS files for details.

Documentation:

• Clarify that -@ starts additional threads in samtools index help, and fix formatting issues in the samtools reset manual page. (PR #2225)

Build changes:

• Added settings to limit memory used by samtools sort when running tests. (PR #2226)

Download the source code here: samtools-1.22.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they don't bundle HTSlib and are missing some generated files.)